The nucleotide sequences of the 5' noncoding region of the GB virus C/hepatitis G virus (GBV- C/HGV) genome was determined in 18 isolates from the United States. Two genotypes have been classified based on the sequence heterogeneity within the 5' noncoding region of GBV-C/HGV. The most distantly related isolates between the two genotypes were 84.6% identical. Sequence identity of the isolates within a genotype were 95-99%. The 5' noncoding region of this virus contains four highly conserved domains. These conserved elements would facilitate the selection of optimal primers for the sensitive detection of GBV-C/HGV RNA by PCR. In addition, they suggest a crucial role for this region in viral replication and/or gene expression. Detection of genotypic variation among GBV-C/HGV infected individuals may provide further insight into the pathogenicity of the virus as well as providing information for the development of effective serological assays.